AutoCloner

Multiple sequence alignment - TraesCS5D01G358300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS5D01G358300	chr5D	100.000	2660	0	0	1	2660	438458292	438455633	0.000000e+00	4913
1	TraesCS5D01G358300	chr5D	82.038	1776	279	28	810	2568	438562572	438560820	0.000000e+00	1476
2	TraesCS5D01G358300	chr5D	80.681	1879	305	28	816	2659	438547562	438545707	0.000000e+00	1406
3	TraesCS5D01G358300	chr5D	78.286	1704	318	40	983	2659	438523718	438522040	0.000000e+00	1050
4	TraesCS5D01G358300	chr5D	88.205	195	20	3	72	265	438441614	438441422	2.060000e-56	230
5	TraesCS5D01G358300	chr5D	77.419	279	55	6	2361	2634	438606025	438605750	2.740000e-35	159
6	TraesCS5D01G358300	chr5B	94.410	1592	72	9	825	2412	533093421	533091843	0.000000e+00	2431
7	TraesCS5D01G358300	chr5B	91.581	487	36	4	352	834	533096255	533095770	0.000000e+00	667
8	TraesCS5D01G358300	chr5B	74.943	1317	300	24	1022	2330	533381539	533380245	6.380000e-161	577
9	TraesCS5D01G358300	chr5B	89.734	263	22	2	2401	2659	533091821	533091560	5.490000e-87	331
10	TraesCS5D01G358300	chr5B	94.595	111	5	1	102	212	533038505	533038396	1.270000e-38	171
11	TraesCS5D01G358300	chr5B	89.394	132	10	1	91	218	533032945	533032814	2.120000e-36	163
12	TraesCS5D01G358300	chrUn	86.161	1438	175	15	718	2144	63333170	63331746	0.000000e+00	1531
13	TraesCS5D01G358300	chrUn	77.839	1999	335	57	711	2659	63296604	63294664	0.000000e+00	1138
14	TraesCS5D01G358300	chrUn	77.800	2000	335	58	711	2659	319150811	319148870	0.000000e+00	1133
15	TraesCS5D01G358300	chrUn	86.158	419	41	5	60	469	63337818	63337408	1.130000e-118	436
16	TraesCS5D01G358300	chrUn	91.333	150	10	2	559	706	63333495	63333347	4.490000e-48	202
17	TraesCS5D01G358300	chrUn	77.955	313	53	12	2354	2659	63397232	63397535	5.850000e-42	182
18	TraesCS5D01G358300	chr5A	86.161	1438	175	15	718	2144	553562405	553560981	0.000000e+00	1531
19	TraesCS5D01G358300	chr5A	79.638	1876	311	44	814	2659	554063248	554061414	0.000000e+00	1282
20	TraesCS5D01G358300	chr5A	95.048	525	23	1	2139	2660	553543168	553542644	0.000000e+00	822
21	TraesCS5D01G358300	chr5A	79.083	1047	176	19	1647	2659	554140989	554139952	0.000000e+00	680
22	TraesCS5D01G358300	chr5A	86.396	419	40	5	60	469	553565960	553565550	2.430000e-120	442
23	TraesCS5D01G358300	chr5A	84.986	353	40	8	58	408	554064358	554064017	1.960000e-91	346
24	TraesCS5D01G358300	chr5A	89.565	230	18	3	479	706	553562807	553562582	1.200000e-73	287
25	TraesCS5D01G358300	chr5A	92.105	76	6	0	40	115	554148768	554148693	1.010000e-19	108
26	TraesCS5D01G358300	chr2A	74.196	1306	287	39	1047	2329	14723334	14722056	1.420000e-137	499

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS5D01G358300	chr5D	438455633	438458292	2659	True	4913.000000	4913	100.000000	1	2660	1	chr5D.!!$R2	2659
1	TraesCS5D01G358300	chr5D	438560820	438562572	1752	True	1476.000000	1476	82.038000	810	2568	1	chr5D.!!$R5	1758
2	TraesCS5D01G358300	chr5D	438545707	438547562	1855	True	1406.000000	1406	80.681000	816	2659	1	chr5D.!!$R4	1843
3	TraesCS5D01G358300	chr5D	438522040	438523718	1678	True	1050.000000	1050	78.286000	983	2659	1	chr5D.!!$R3	1676
4	TraesCS5D01G358300	chr5B	533091560	533096255	4695	True	1143.000000	2431	91.908333	352	2659	3	chr5B.!!$R4	2307
5	TraesCS5D01G358300	chr5B	533380245	533381539	1294	True	577.000000	577	74.943000	1022	2330	1	chr5B.!!$R3	1308
6	TraesCS5D01G358300	chrUn	63294664	63296604	1940	True	1138.000000	1138	77.839000	711	2659	1	chrUn.!!$R1	1948
7	TraesCS5D01G358300	chrUn	319148870	319150811	1941	True	1133.000000	1133	77.800000	711	2659	1	chrUn.!!$R2	1948
8	TraesCS5D01G358300	chrUn	63331746	63337818	6072	True	723.000000	1531	87.884000	60	2144	3	chrUn.!!$R3	2084
9	TraesCS5D01G358300	chr5A	553542644	553543168	524	True	822.000000	822	95.048000	2139	2660	1	chr5A.!!$R1	521
10	TraesCS5D01G358300	chr5A	554061414	554064358	2944	True	814.000000	1282	82.312000	58	2659	2	chr5A.!!$R5	2601
11	TraesCS5D01G358300	chr5A	553560981	553565960	4979	True	753.333333	1531	87.374000	60	2144	3	chr5A.!!$R4	2084
12	TraesCS5D01G358300	chr5A	554139952	554140989	1037	True	680.000000	680	79.083000	1647	2659	1	chr5A.!!$R2	1012
13	TraesCS5D01G358300	chr2A	14722056	14723334	1278	True	499.000000	499	74.196000	1047	2329	1	chr2A.!!$R1	1282

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
163	168	0.107508	AGTGACGATGGCATCCCAAG	60.108	55.0	21.2	9.95	46.14	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1888	8342	0.957395	ATTCAGCAGACGGCCACTTG	60.957	55.0	2.24	0.0	46.5	3.16	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	5.827568	GCGAAGAAAAAGCAATTCAATGA	57.172	34.783	0.00	0.00	0.00	2.57
23	24	5.840250	GCGAAGAAAAAGCAATTCAATGAG	58.160	37.500	0.00	0.00	0.00	2.90
24	25	5.164022	GCGAAGAAAAAGCAATTCAATGAGG	60.164	40.000	0.00	0.00	0.00	3.86
25	26	5.922544	CGAAGAAAAAGCAATTCAATGAGGT	59.077	36.000	0.00	0.00	0.00	3.85
26	27	6.421801	CGAAGAAAAAGCAATTCAATGAGGTT	59.578	34.615	0.00	0.00	0.00	3.50
27	28	7.486802	AAGAAAAAGCAATTCAATGAGGTTG	57.513	32.000	6.21	6.21	39.25	3.77
28	29	6.585416	AGAAAAAGCAATTCAATGAGGTTGT	58.415	32.000	10.59	0.00	38.95	3.32
29	30	6.480981	AGAAAAAGCAATTCAATGAGGTTGTG	59.519	34.615	10.59	0.00	38.95	3.33
30	31	3.308438	AGCAATTCAATGAGGTTGTGC	57.692	42.857	10.59	5.40	37.51	4.57
31	32	2.895404	AGCAATTCAATGAGGTTGTGCT	59.105	40.909	10.59	7.14	40.67	4.40
32	33	3.057033	AGCAATTCAATGAGGTTGTGCTC	60.057	43.478	10.59	0.00	41.24	4.26
33	34	3.841643	CAATTCAATGAGGTTGTGCTCC	58.158	45.455	3.32	0.00	38.95	4.70
34	35	2.655090	TTCAATGAGGTTGTGCTCCA	57.345	45.000	0.00	0.00	38.95	3.86
35	36	2.655090	TCAATGAGGTTGTGCTCCAA	57.345	45.000	0.00	0.00	38.95	3.53
36	37	2.942804	TCAATGAGGTTGTGCTCCAAA	58.057	42.857	0.00	0.00	38.95	3.28
37	38	2.622942	TCAATGAGGTTGTGCTCCAAAC	59.377	45.455	0.00	0.00	41.34	2.93
38	39	2.361757	CAATGAGGTTGTGCTCCAAACA	59.638	45.455	7.35	2.68	43.60	2.83
39	40	2.136298	TGAGGTTGTGCTCCAAACAA	57.864	45.000	7.35	0.00	43.60	2.83
40	41	2.451490	TGAGGTTGTGCTCCAAACAAA	58.549	42.857	7.35	0.00	43.60	2.83
41	42	3.030291	TGAGGTTGTGCTCCAAACAAAT	58.970	40.909	7.35	0.00	43.60	2.32
42	43	3.450457	TGAGGTTGTGCTCCAAACAAATT	59.550	39.130	7.35	0.00	43.60	1.82
43	44	4.081198	TGAGGTTGTGCTCCAAACAAATTT	60.081	37.500	7.35	0.00	43.60	1.82
44	45	5.127845	TGAGGTTGTGCTCCAAACAAATTTA	59.872	36.000	7.35	0.00	43.60	1.40
45	46	5.983540	AGGTTGTGCTCCAAACAAATTTAA	58.016	33.333	7.35	0.00	43.60	1.52
46	47	6.591001	AGGTTGTGCTCCAAACAAATTTAAT	58.409	32.000	7.35	0.00	43.60	1.40
47	48	7.731054	AGGTTGTGCTCCAAACAAATTTAATA	58.269	30.769	7.35	0.00	43.60	0.98
48	49	8.207545	AGGTTGTGCTCCAAACAAATTTAATAA	58.792	29.630	7.35	0.00	43.60	1.40
49	50	8.831550	GGTTGTGCTCCAAACAAATTTAATAAA	58.168	29.630	0.00	0.00	40.67	1.40
163	168	0.107508	AGTGACGATGGCATCCCAAG	60.108	55.000	21.20	9.95	46.14	3.61
226	231	3.937706	CTCTCAACCACTCCAAGCTAATG	59.062	47.826	0.00	0.00	0.00	1.90
290	299	4.836125	ATTCGACATGTGGATAAATGCC	57.164	40.909	11.61	0.00	0.00	4.40
364	374	0.607489	AAGGCTCGATGCAAGCAACT	60.607	50.000	10.85	0.00	45.15	3.16
386	398	1.341285	TGGTGCAGCATCAATAGCCTT	60.341	47.619	15.99	0.00	0.00	4.35
423	489	0.820891	GGCCATTGAGCATGTCCGAT	60.821	55.000	0.00	0.00	0.00	4.18
476	542	2.584608	CACCACCATCGTCCCCTC	59.415	66.667	0.00	0.00	0.00	4.30
517	3844	2.038820	CCCAGTTTGCCCAACAATTGAT	59.961	45.455	13.59	0.00	38.31	2.57
518	3845	3.068560	CCAGTTTGCCCAACAATTGATG	58.931	45.455	13.59	10.86	38.31	3.07
539	3866	2.799126	ACTGGGATTCAACCGCATAA	57.201	45.000	0.00	0.00	0.00	1.90
548	4117	3.980646	TCAACCGCATAATTGCCATAC	57.019	42.857	0.00	0.00	46.57	2.39
664	4556	0.745845	AGCAATGCACTCGACATCCC	60.746	55.000	8.35	0.00	0.00	3.85
685	4577	4.827284	CCCTGGTGACTTAAAGAACAATGT	59.173	41.667	0.00	0.00	0.00	2.71
714	4764	9.649316	AACAATTCTAGCTATCTAGGAGTAGTT	57.351	33.333	0.00	0.00	42.01	2.24
755	4814	0.974010	ATTCCAATGTGGGCAGCTGG	60.974	55.000	17.12	0.00	38.32	4.85
772	4831	5.068987	GCAGCTGGATTATAAATCCCAACAA	59.931	40.000	17.12	0.00	37.40	2.83
774	4833	6.980397	CAGCTGGATTATAAATCCCAACAAAC	59.020	38.462	14.53	0.00	37.40	2.93
776	4835	6.405397	GCTGGATTATAAATCCCAACAAACGT	60.405	38.462	14.53	0.00	37.40	3.99
790	4849	2.743126	ACAAACGTCGACTTGGAAAACA	59.257	40.909	18.44	0.00	0.00	2.83
889	7317	2.487762	CCTGCGAGCATTTTGTCCTTTA	59.512	45.455	0.00	0.00	0.00	1.85
890	7318	3.492313	CTGCGAGCATTTTGTCCTTTAC	58.508	45.455	0.00	0.00	0.00	2.01
1069	7514	0.538057	CCTGCCTTTGAGTGCTTCCA	60.538	55.000	0.00	0.00	0.00	3.53
1104	7549	4.189580	GGCAAGCCGCTATCCCCA	62.190	66.667	0.00	0.00	41.91	4.96
1107	7552	2.366972	AAGCCGCTATCCCCAGGT	60.367	61.111	0.00	0.00	0.00	4.00
1470	7921	1.078848	GTGGCAGAGCTTCGACCAT	60.079	57.895	0.00	0.00	30.88	3.55
1541	7992	3.061260	GAGGCACTACCGACCGTCC	62.061	68.421	0.00	0.00	46.52	4.79
1888	8342	3.315191	CGTTGGTGTGGGATATCATTTCC	59.685	47.826	4.83	0.00	0.00	3.13
2019	8476	1.692411	GCAAACAAGGAGGAGTGGTT	58.308	50.000	0.00	0.00	0.00	3.67
2499	9030	0.957395	AGGATTGTGCTGCCAGTTCG	60.957	55.000	0.00	0.00	0.00	3.95
2531	9062	8.090831	GTGGTCTTCTCATACTCATATGCATAA	58.909	37.037	11.13	0.00	38.50	1.90
2602	9141	7.216973	ACAATAATGTTTTAGTTTACGGCCA	57.783	32.000	2.24	0.00	35.91	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.164022	CCTCATTGAATTGCTTTTTCTTCGC	60.164	40.000	0.00	0.00	0.00	4.70
1	2	5.922544	ACCTCATTGAATTGCTTTTTCTTCG	59.077	36.000	0.00	0.00	0.00	3.79
2	3	7.225341	ACAACCTCATTGAATTGCTTTTTCTTC	59.775	33.333	9.26	0.00	41.23	2.87
3	4	7.011669	CACAACCTCATTGAATTGCTTTTTCTT	59.988	33.333	9.26	0.00	41.23	2.52
4	5	6.480981	CACAACCTCATTGAATTGCTTTTTCT	59.519	34.615	9.26	0.00	41.23	2.52
5	6	6.652245	CACAACCTCATTGAATTGCTTTTTC	58.348	36.000	9.26	0.00	41.23	2.29
6	7	5.007921	GCACAACCTCATTGAATTGCTTTTT	59.992	36.000	9.26	0.00	41.23	1.94
7	8	4.512571	GCACAACCTCATTGAATTGCTTTT	59.487	37.500	9.26	0.00	41.23	2.27
8	9	4.060205	GCACAACCTCATTGAATTGCTTT	58.940	39.130	9.26	0.00	41.23	3.51
9	10	3.322828	AGCACAACCTCATTGAATTGCTT	59.677	39.130	9.26	0.00	42.49	3.91
10	11	2.895404	AGCACAACCTCATTGAATTGCT	59.105	40.909	9.26	6.00	41.13	3.91
11	12	3.248266	GAGCACAACCTCATTGAATTGC	58.752	45.455	9.26	4.24	41.23	3.56
12	13	3.256383	TGGAGCACAACCTCATTGAATTG	59.744	43.478	8.19	8.19	41.23	2.32
13	14	3.499338	TGGAGCACAACCTCATTGAATT	58.501	40.909	0.00	0.00	41.23	2.17
14	15	3.159213	TGGAGCACAACCTCATTGAAT	57.841	42.857	0.00	0.00	41.23	2.57
15	16	2.655090	TGGAGCACAACCTCATTGAA	57.345	45.000	0.00	0.00	41.23	2.69
16	17	2.622942	GTTTGGAGCACAACCTCATTGA	59.377	45.455	0.00	0.00	41.23	2.57
17	18	2.361757	TGTTTGGAGCACAACCTCATTG	59.638	45.455	0.00	0.00	44.60	2.82
18	19	2.665165	TGTTTGGAGCACAACCTCATT	58.335	42.857	0.00	0.00	39.19	2.57
19	20	2.363306	TGTTTGGAGCACAACCTCAT	57.637	45.000	0.00	0.00	39.19	2.90
20	21	2.136298	TTGTTTGGAGCACAACCTCA	57.864	45.000	0.00	0.00	39.19	3.86
21	22	3.733443	ATTTGTTTGGAGCACAACCTC	57.267	42.857	0.00	0.00	39.19	3.85
22	23	4.486125	AAATTTGTTTGGAGCACAACCT	57.514	36.364	0.00	0.00	39.19	3.50
23	24	6.859420	ATTAAATTTGTTTGGAGCACAACC	57.141	33.333	0.00	0.00	39.19	3.77
52	53	9.010366	GCGTTGGATCTTGTTAGAAATAAAATC	57.990	33.333	0.00	0.00	33.20	2.17
53	54	8.519526	TGCGTTGGATCTTGTTAGAAATAAAAT	58.480	29.630	0.00	0.00	33.20	1.82
54	55	7.877003	TGCGTTGGATCTTGTTAGAAATAAAA	58.123	30.769	0.00	0.00	33.20	1.52
55	56	7.441890	TGCGTTGGATCTTGTTAGAAATAAA	57.558	32.000	0.00	0.00	33.20	1.40
56	57	7.465379	CGATGCGTTGGATCTTGTTAGAAATAA	60.465	37.037	0.00	0.00	33.20	1.40
163	168	1.004277	CTCAGCTGTTCACGTCGGAC	61.004	60.000	14.67	0.00	0.00	4.79
269	278	4.836125	GGCATTTATCCACATGTCGAAT	57.164	40.909	0.00	0.00	0.00	3.34
285	294	1.289109	CGACAACTCGTTCCGGCATT	61.289	55.000	0.00	0.00	35.00	3.56
290	299	0.595567	TGTTCCGACAACTCGTTCCG	60.596	55.000	0.00	0.00	38.32	4.30
336	345	0.798776	CATCGAGCCTTGGTCACAAC	59.201	55.000	0.00	0.00	32.14	3.32
364	374	2.107031	AGGCTATTGATGCTGCACCATA	59.893	45.455	3.57	0.79	0.00	2.74
386	398	1.948611	GCCAATCAAACCGTAGCCAGA	60.949	52.381	0.00	0.00	0.00	3.86
395	407	1.275856	TGCTCAATGGCCAATCAAACC	59.724	47.619	10.96	0.00	0.00	3.27
397	409	2.568062	ACATGCTCAATGGCCAATCAAA	59.432	40.909	10.96	0.00	40.94	2.69
423	489	3.160585	CCAGGGACAAGCCAGTCA	58.839	61.111	8.23	0.00	40.29	3.41
490	3806	2.168728	TGTTGGGCAAACTGGGTTTAAC	59.831	45.455	6.28	0.00	39.70	2.01
517	3844	0.687920	TGCGGTTGAATCCCAGTACA	59.312	50.000	0.00	0.00	0.00	2.90
518	3845	2.038387	ATGCGGTTGAATCCCAGTAC	57.962	50.000	0.00	0.00	0.00	2.73
539	3866	0.250901	GGCCTGGATCGTATGGCAAT	60.251	55.000	15.34	0.00	46.53	3.56
548	4117	4.227134	CTGACCCGGCCTGGATCG	62.227	72.222	21.63	3.16	42.00	3.69
664	4556	9.233232	GTTTAACATTGTTCTTTAAGTCACCAG	57.767	33.333	5.07	0.00	0.00	4.00
693	4585	7.975608	TGCTAACTACTCCTAGATAGCTAGAA	58.024	38.462	16.63	0.00	45.33	2.10
714	4764	0.677731	GGCTGCCAACATCACTGCTA	60.678	55.000	15.17	0.00	0.00	3.49
755	4814	6.903479	GTCGACGTTTGTTGGGATTTATAATC	59.097	38.462	0.00	0.00	0.00	1.75
772	4831	2.348660	TGTGTTTTCCAAGTCGACGTT	58.651	42.857	10.46	2.10	0.00	3.99
774	4833	2.350498	AGTTGTGTTTTCCAAGTCGACG	59.650	45.455	10.46	0.00	0.00	5.12
776	4835	3.869065	AGAGTTGTGTTTTCCAAGTCGA	58.131	40.909	0.00	0.00	43.72	4.20
889	7317	1.523758	GCGTGGAACCTTGATCTTGT	58.476	50.000	0.00	0.00	0.00	3.16
890	7318	0.804989	GGCGTGGAACCTTGATCTTG	59.195	55.000	0.00	0.00	0.00	3.02
895	7323	1.227823	CACTGGCGTGGAACCTTGA	60.228	57.895	2.23	0.00	37.50	3.02
964	7399	6.749118	GCCAAAATCTTAATCACTAAGCTGTG	59.251	38.462	0.00	0.00	37.51	3.66
1069	7514	4.324991	GGGGACAAGGCGGTCGTT	62.325	66.667	6.32	0.00	38.70	3.85
1104	7549	2.492484	GTCAGAGACGATGGTTGTACCT	59.508	50.000	0.00	0.00	39.58	3.08
1470	7921	3.047718	GAGGATCGTGTCGGTGCGA	62.048	63.158	0.00	0.00	41.50	5.10
1606	8057	4.754667	GGTTCGAGGGGCGTGTCC	62.755	72.222	0.00	0.00	41.80	4.02
1607	8058	2.798148	AATGGTTCGAGGGGCGTGTC	62.798	60.000	0.00	0.00	41.80	3.67
1888	8342	0.957395	ATTCAGCAGACGGCCACTTG	60.957	55.000	2.24	0.00	46.50	3.16
2019	8476	1.228245	GCCAAGAACCTGCCACTGA	60.228	57.895	0.00	0.00	0.00	3.41
2378	8868	6.614162	GCACATTAGCAAAGACAAAATCAACG	60.614	38.462	0.00	0.00	0.00	4.10
2499	9030	2.166664	AGTATGAGAAGACCACCGCTTC	59.833	50.000	0.00	0.00	41.53	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.